CoverageExperiment

#' @description

Usage

CoverageExperiment(tracks, features, ...)

coarsen(x, window, ...)

# S4 method for class 'BigWigFileList,GRangesList'
CoverageExperiment(
  tracks,
  features,
  width = NULL,
  center = FALSE,
  scale = FALSE,
  ignore.strand = TRUE,
  window = 1,
  BPPARAM = BiocParallel::bpparam()
)

# S4 method for class 'BigWigFileList,GRanges'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'BigWigFileList,list'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'BigWigFile,GRangesList'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'BigWigFile,GRanges'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'BigWigFile,list'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'list,GRangesList'
CoverageExperiment(
  tracks,
  features,
  width = NULL,
  center = FALSE,
  scale = FALSE,
  ignore.strand = TRUE,
  window = 1,
  BPPARAM = BiocParallel::bpparam()
)

# S4 method for class 'list,GRanges'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'list,list'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'RleList,GRangesList'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'RleList,GRanges'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'RleList,list'
CoverageExperiment(tracks, features, ...)

# S4 method for class 'CoverageExperiment'
coarsen(x, window = 1, BPPARAM = BiocParallel::bpparam())

Arguments

tracks

A genomic track imported as a RleList or a named list of genomic tracks.

features

A set of features imported as GRanges or a named GRangesList.

...

Passed to the relevant method

x

a CoverageExperiment object

window

an integer to coarsen coverage by.

width

Width to resize each set of genomic features

scale, center

Logical, whether to scale and/or center tracks prior to summarization

ignore.strand

Logical, whether to not take the features strand information

BPPARAM

Passed to BiocParallel.

Value

A CoverageExperiment object

Details

CoverageExperiment objects store coverages for individual tracks over different sets of features. The coverage assay contains a separate matrix for each combination of track x features. CoverageExperiment objects are instantiated using the CoverageExperiment() #' function, and can be coarsened using the coarsen() function.

Examples

library(rtracklayer)
library(purrr)
#> 
#> Attaching package: ‘purrr’
#> The following object is masked from ‘package:GenomicRanges’:
#> 
#>     reduce
#> The following object is masked from ‘package:IRanges’:
#> 
#>     reduce
library(plyranges)
#> 
#> Attaching package: ‘plyranges’
#> The following object is masked from ‘package:IRanges’:
#> 
#>     slice
#> The following object is masked from ‘package:stats’:
#> 
#>     filter
TSSs_bed <- system.file("extdata", "TSSs.bed", package = "tidyCoverage")
features <- import(TSSs_bed) |> filter(strand == '+')

#############################################################################
## 1. Creating a `CoverageExperiment` object from a single BigWigFile
#############################################################################

RNA_fwd <- system.file("extdata", "RNA.fwd.bw", package = "tidyCoverage")
tracks <- BigWigFile(RNA_fwd)
CoverageExperiment(tracks, features, width = 5000)
#> class: CoverageExperiment 
#> dim: 1 1 
#> metadata(0):
#> assays(1): coverage
#> rownames(1): features
#> rowData names(2): features n
#> colnames(1): track
#> colData names(1): track
#> width: 5000

#############################################################################
## 2. Creating a `CoverageExperiment` object from a BigWigFileList
#############################################################################

RNA_rev <- system.file("extdata", "RNA.rev.bw", package = "tidyCoverage")
tracks <- BigWigFileList(list(RNA_fwd = RNA_fwd, RNA_rev = RNA_rev))
CoverageExperiment(tracks, features, width = 5000)
#> class: CoverageExperiment 
#> dim: 1 2 
#> metadata(0):
#> assays(1): coverage
#> rownames(1): features
#> rowData names(2): features n
#> colnames(2): RNA_fwd RNA_rev
#> colData names(1): track
#> width: 5000

#############################################################################
## 3. Creating a `CoverageExperiment` object from imported bigwig files
#############################################################################

tracks <- list(
    RNA_fwd = system.file("extdata", "RNA.fwd.bw", package = "tidyCoverage"),
    RNA_rev = system.file("extdata", "RNA.rev.bw", package = "tidyCoverage")
) |> map(import, as = 'Rle')
CoverageExperiment(tracks, features, width = 5000)
#> class: CoverageExperiment 
#> dim: 1 2 
#> metadata(0):
#> assays(1): coverage
#> rownames(1): features
#> rowData names(2): features n
#> colnames(2): RNA_fwd RNA_rev
#> colData names(1): track
#> width: 5000

#############################################################################
## 4. Correct for strandness when recovering coverage
#############################################################################

TSSs_bed <- system.file("extdata", "TSSs.bed", package = "tidyCoverage")
features <- list(
    TSS_fwd = import(TSSs_bed) |> filter(strand == '+'), 
    TSS_rev = import(TSSs_bed) |> filter(strand == '-')
)
tracks <- list(
    RNA_fwd = system.file("extdata", "RNA.fwd.bw", package = "tidyCoverage"),
    RNA_rev = system.file("extdata", "RNA.rev.bw", package = "tidyCoverage")
) |> map(import, as = 'Rle')
CoverageExperiment(tracks, features, width = 5000, ignore.strand = FALSE)
#> class: CoverageExperiment 
#> dim: 2 2 
#> metadata(0):
#> assays(1): coverage
#> rownames(2): TSS_fwd TSS_rev
#> rowData names(2): features n
#> colnames(2): RNA_fwd RNA_rev
#> colData names(1): track
#> width: 5000

#############################################################################
## Aggregating a `CoverageExperiment` object
#############################################################################
data(ce)
coarsen(ce, window = 10)
#> class: CoverageExperiment 
#> dim: 1 2 
#> metadata(0):
#> assays(1): coverage
#> rownames(1): Scc1
#> rowData names(2): features n
#> colnames(2): RNA_fwd RNA_rev
#> colData names(1): track
#> width: 3000